The Araguaia River Basin is located in Central Brazil and presents a wide diversity of natural landscapes, as well as an important transition zone between the Cerrado and Amazon biomes. A large alluvial plain extends throughout the middle Araguaia, where the largest fluvial island in the world is formed and a set of wetlands that are essential in regulating the water and climate balance, and for local biodiversity. In Brazil, these areas have been constantly under threat mainly due to the expansion of the agricultural frontier and deforestation associated with significant emissions of carbon dioxide to the atmosphere. The monitoring and detection of environmental changes become increasingly large, however, little is known about the spacetime variability of the carbon cycle in these areas. The primary productivity of vegetation is one of the most relevant processes to assess global carbon balance and climate change on a regional and global scale and can be estimated through remote sensing data. The objective of this study was to understand the role of relief and land cover on the annual seasonality of gross primary productivity in the Araguaia basin. The primary data corresponded to topographic data, land cover map, and gross primary productivity (GPP) data generated from a 15-year time series of the MODIS2A2HV6 product of the Moderate Resolution Imaging Spectroradiometer (MODIS) sensor. We observed that pastures present a wide and heterogeneous distribution throughout the Araguaia river basin, while the agricultural areas are mainly concentrated in relatively old, high and flat topographies, which may represent a negative factor for the conservation of the region. Field and savanna formations present less contribution to the amount of carbon sequestration, but a good part of the carbon stocks in the Cerrado biome are not found in the aerial compartment of the vegetation, which may be addressed in future studies. Forest areas presented the highest annual mean GPPs over the period, proving to be a key component for estimating carbon sequestration at regional and global scales.